GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pedobacter sp. GW460-11-11-14-LB5

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate CA265_RS25430 CA265_RS25430 UDP-glucose 4-epimerase GalE

Query= uniprot:L0FXG3
         (337 letters)



>FitnessBrowser__Pedo557:CA265_RS25430
          Length = 340

 Score =  364 bits (935), Expect = e-105
 Identities = 183/338 (54%), Positives = 238/338 (70%), Gaps = 4/338 (1%)

Query: 1   MQQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDC 60
           M +IL+TGG GYIGSHTAV L NAGYE +IVDN SNSN ++L  L  I G    +HE D 
Sbjct: 1   MAKILVTGGTGYIGSHTAVELHNAGYEVVIVDNLSNSNIKILTQLHAITGKWFDFHEIDL 60

Query: 61  NDRKFMQAVFEEN-DLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKD 119
            D + +Q   E + D+ G+IHFAASKAVGES + PL YY NN   LI LL +  +    +
Sbjct: 61  QDDRAVQEFAENHTDIDGIIHFAASKAVGESVEQPLKYYKNNFYGLINLLTSFNR--KIN 118

Query: 120 IVFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYF 179
            VFSSSCTVYGQP+ LPV E  P + AESPYGNTK+I E+IL +         ++ALRYF
Sbjct: 119 FVFSSSCTVYGQPETLPVTEAAPVQKAESPYGNTKQIAEEILAETAAVTPALNIIALRYF 178

Query: 180 NPIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMD 239
           NP+GAH ++LIGELP GVPANL+PF+TQ+  G R  ITV+GDDY+TPDG+ IRDYIHV+D
Sbjct: 179 NPVGAHETALIGELPNGVPANLVPFITQSAIGKRGPITVYGDDYDTPDGSAIRDYIHVVD 238

Query: 240 LADAHVKSIQYLAD-QPENFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGD 298
           LA AHV +I+ L +  P    D+FN+GTG G++V+E+I AFEKV+ + L+Y+IGPRR+GD
Sbjct: 239 LAKAHVAAIKKLEEGNPNGNYDVFNIGTGKGSSVLEIIAAFEKVNGEKLDYKIGPRRAGD 298

Query: 299 IEKVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLK 336
           I +++ +  K +  LGW     + E +R AW W+  +K
Sbjct: 299 IVQIYGDVQKSNNELGWKANLDINEMMRSAWEWEKYIK 336


Lambda     K      H
   0.316    0.136    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 398
Number of extensions: 18
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 337
Length of database: 340
Length adjustment: 28
Effective length of query: 309
Effective length of database: 312
Effective search space:    96408
Effective search space used:    96408
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate CA265_RS25430 CA265_RS25430 (UDP-glucose 4-epimerase GalE)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01179.hmm
# target sequence database:        /tmp/gapView.17149.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01179  [M=332]
Accession:   TIGR01179
Description: galE: UDP-glucose 4-epimerase GalE
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                  Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   5.9e-123  395.9   0.1   6.6e-123  395.7   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS25430  CA265_RS25430 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS25430  CA265_RS25430 UDP-glucose 4-epimerase GalE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.7   0.1  6.6e-123  6.6e-123       1     329 [.       3     336 ..       3     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 395.7 bits;  conditional E-value: 6.6e-123
                                  TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavl 66 
                                                kiLvtGg+GyiGsh++++l ++g+evv++Dnls+++ ++l++l+ it   + + e dl+d ++++++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS25430   3 KILVTGGTGYIGSHTAVELHNAGYEVVIVDNLSNSNIKILTQLHAITgkWFDFHEIDLQDDRAVQEFA 70 
                                                79********************************************998899**************99 PP

                                  TIGR01179  67 e.eekidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpi 133
                                                e +++id +iHfaa++avgEsv++PlkYY+nn  + ++Ll + ++    +++Fsss++vYg++e++p+
  lcl|FitnessBrowser__Pedo557:CA265_RS25430  71 EnHTDIDGIIHFAASKAVGESVEQPLKYYKNNFYGLINLLTSFNR--KINFVFSSSCTVYGQPETLPV 136
                                                83458***********************************99976..579****************** PP

                                  TIGR01179 134 sEespln.pinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklv 199
                                                +E++p++ +++pYG++k ++E+il +++ + ++l++++LRYFn++GA+e   iGe +++ + +l++ +
  lcl|FitnessBrowser__Pedo557:CA265_RS25430 137 TEAAPVQkAESPYGNTKQIAEEILAETAAVTPALNIIALRYFNPVGAHETALIGELPNGVPaNLVPFI 204
                                                *****9989*********************************************************** PP

                                  TIGR01179 200 aevavgkrekleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeg...gesevynlGagqgfsv 264
                                                ++ a+gkr  ++++G+dy+t+DG ++RDyiHv Dla+aH+aa+++leeg   g+++v+n+G+g+g sv
  lcl|FitnessBrowser__Pedo557:CA265_RS25430 205 TQSAIGKRGPITVYGDDYDTPDGSAIRDYIHVVDLAKAHVAAIKKLEEGnpnGNYDVFNIGTGKGSSV 272
                                                ***********************************************985545899************ PP

                                  TIGR01179 265 kevieavkkvsgkdikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklk 329
                                                +e+i a++kv g+++ +++ +rRaGD+ ++++d +k ++elgwk+++d ++e+++saw+Wek +k
  lcl|FitnessBrowser__Pedo557:CA265_RS25430 273 LEIIAAFEKVNGEKLDYKIGPRRAGDIVQIYGDVQKSNNELGWKANLD-INEMMRSAWEWEKYIK 336
                                                ***********************************************9.************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (340 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.56
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory